Statistical analyses of complex denaturing gradient gel electrophoresis profiles

The gut-brain-axis: A positive relationship between gut microbial dysbiosis and glioblastoma brain tumour

The glioblastoma brain tumour (GBM) stands out as the most aggressive and resistant-to-treatment malignancy. Nevertheless, the gut-brain connection plays a pivotal role in influencing the growth and activation of the central nervous system. In this particular investigation, we aimed to assess and characterize the gut microbial ecosystem in GBM patients, both quantitatively and qualitatively. We collected faecal samples from 15 healthy volunteers and 25 GBM patients. To delve into the microbial content, we employed PCR-DGGE, targeting the V3 region of the 16S rRNA gene, and conducted qPCR to measure the levels of crucial intestinal bacteria. For a more in-depth analysis, high-throughput sequencing was performed on a selection of 20 random faecal samples (10 from healthy individuals and 10 from GBM patients), targeting the V3+V4 region of the 16S rRNA gene. Our findings from examining the richness and diversity of the gut microbiota unveiled that GBM patients exhibited significantly higher microbial diversity compared to healthy individuals. At the phylum level, Proteobacteria saw a significant increase, while Firmicutes experienced a noteworthy decrease in the GBM group. Moving down to the family level, we observed significantly elevated levels of Enterobacteriaceae, Bacteroidaceae, and Lachnospiraceae in GBM patients, while levels of Veillonellaceae, Rikenellaceae, and Prevotellaceae were notably lower. Delving into genera statistics, we noted a substantial increase in the abundance of Parasutterella, Escherichia-Shigella, and Bacteroides, alongside significantly lower levels of Ruminococcus 2, Faecalibacterium, and Prevotella_9 in the GBM group compared to the control group. Furthermore, when examining specific species, we found a significant increase in Bacteroides vulgatus and Escherichia coli in the GBM group. These observations collectively indicate a marked dysbiosis in the gut microbial composition of GBM patients. Additionally, the GBM group exhibited notably higher levels of alpha diversity when compared to the control group. This increase in diversity suggests a significant bacterial overgrowth in the gut of GBM patients in contrast to the controls. As a result, this research opens up potential avenues to gain a better understanding of the underlying mechanisms, pathways, and potential treatments for GBM, stemming from the significant implications of gut microbial dysbiosis in these patients.

Multi-Omics Analysis Demonstrates the Critical Role of Non-Ethanolic Components of Alcoholic Beverages in the Host Microbiome and Metabolome: A Human- and Animal-Based Study

It is known that alcoholic beverages alter the human gut microbiome. This study focused on the potential impact of non-ethanolic ingredients in whisky on the gut bacteriome. A pilot study was carried out on 15 whisky drinkers, 5 rice beer drinkers, and 9 non-drinkers to determine the effect of alcoholic beverages on the host microbiome and metabolome. Additionally, a mouse model was used to assess the differential impact of three whisky brands (each with an equal ethanol concentration). The results indicate that the non-ethanolic components have an impact on the gut microbiome, as well as on the metabolites in blood and feces. The amount of Prevotella copri, a typical core Indian gut bacterium, decreased in both the human and mouse groups of whisky type 1, but an increase in abundance of Helicobacteriaceae (p = 0.01) was noticed in both groups. Additionally, the alcohol-treated cohorts had lower levels of short-chain fatty acids (SCFAs), specifically butyric acid, and higher amounts of lipids and stress marker IL1-ß than the untreated groups (p = 0.04-0.01). Furthermore, two compounds, ethanal/acetaldehyde (found in all the whisky samples) and arabitol (unique to whisky type 1), were tested in the mice. Similar to the human subjects, the whisky type 1 treated mouse cohort and the arabitol-treated group showed decreased levels of Prevotella copri (p = 0.01) in their gut. The results showed that non-ethanolic compounds have a significant impact on host gut bacterial diversity and metabolite composition, which has a further vital impact on host health. Our work further emphasizes the need to study the impact of non-ethanolic ingredients of alcoholic beverages on host health.

Effectiveness of the Human Oral Microbe Identification Microarray in Identifying Periodontal Pathogens: A Systematic Review

The aim of this review was to investigate the effectiveness of the Human Oral Microbe Identification Microarray (HOMIM) in identifying and quantifying bacterial species of the oral microbiome in periodontal disease. The search for articles was conducted in CENTRAL, CINAHL, MEDLINE and EMBASE by two reviewers, and included articles published in English between January 1990 and December 2021. The selected articles were human observational studies in adults between 18 and 65 years, presenting specific predefined keywords. Articles were initially selected by title and abstract; articles that met the inclusion criteria were analyzed for methodological quality using a detailed checklist for quality assessment. Data were extracted and reported using the PRISMA tool. The study design, sample, follow-up period, collection and microbial analysis methods, statistical treatment, results and discussion were quality assessed and risk of bias was evaluated using the Cochrane Risk-of-Bias tool. A narrative synthesis approach was used to synthesize and interpret the extracted data. From the initial search, 2931 articles were retrieved; 51 of these were then selected after screening by title and abstract. Subsequently, 8 articles met the inclusion after full-text reading and were classed according to methodological quality as high (2), moderate (3) or low (3). Studies included in this review were of high and medium quality. Data from the Human Oral Microbe Identification Microarray (HOMIM) provide much more robust results, showing major shifts between periodontal health and periodontal disease. Compared to earlier techniques such as Denaturing Gradient Gel Electrophoresis (DGGE), HOMIM represents a more effective approach for quantification due to its high sensitivity; thus, it is able to identify a high prevalence of periodontal pathogens and novel species in low abundance. The literature provides moderate evidence that the Human Oral Microbe Identification Microarray (HOMIM) is more effective in identifying and quantifying bacterial species of the oral microbiome in periodontal disease, compared to earlier molecular and non-molecular methods such as Denaturing Gradient Gel Electrophoresis (DGGE) and a culture-based approach with phenotypic tests.

Contrasting Water Quality Treatments Result in Structural and Functional Changes to Wetland Plant-Associated Microbial Communities in Lab-Scale Mesocosms

The impact of contrasting water quality treatments on wetland plant-associated microbial communities was investigated in this study using 12 lab-scale wetland mesocosms (subsurface flow design) planted with reed canary grass (Phalaris arundinacea) or water speedwell (Veronica anagallis-aquatica) over a 13-week period. Mesocosms received water collected from two sites along the Grand River (Ontario, Canada) designated as having either high or poor water quality according to Grand River Conservation Authority classifications. All mesocosms were established using sediment collected from the high water quality site and received water from this source pre-treatment. Resulting changes to microbial community structure were assessed using PCR-denaturing gel gradient electrophoresis (DGGE) on microbial 16S rDNA sequences extracted from rhizoplane, rhizosphere, and water samples before and after exposure to water quality treatments. Functional community changes were determined using Biolog™ EcoPlates which assess community-level carbon source utilization profiles. Wetland mesocosm removal of inorganic nutrients (N, P) and fecal coliforms was also determined, and compared among treatments. Treatment-specific effects were assessed using a repeated measures restricted maximum likelihood (REML) analysis. Structural and functional characteristics of rhizoplane microbial communities were significantly influenced by the interaction between plant species and water treatment (P = 0.04, P = 0.01). Plant species-specific effects were observed for rhizosphere structural diversity (P = 0.01) and wetland water community metabolic diversity (P = 0.03). The effect of water treatment alone was significant for structural diversity measurements in wetland water communities (P = 0.03). The effect of plant species, water quality treatment, and the interaction between the two is dependent on the microhabitat type (rhizoplane, rhizosphere, or water). Rhizoplane communities appear to be more sensitive to water quality-specific environmental changes and may be a good candidate for microbial community-based monitoring of wetland ecosystems.

Typical indigenous bacteria in the cecum of ddY mice fed a casein-beef tallow diet or whole-egg diet

With the aim to prove the existence of food ingredient-susceptible indigenous bacteria (SIBs) in the gut, the gut microbiota of ddY mice fed a diet containing 20% milk casein and 17% beef tallow (CT diet) or 40% whole-egg powder (Egg diet) for 14 days were analyzed by 16S ribosomal RNA gene (V4) amplicon sequencing. At the genus level, abundance levels of Desulfovibrionaceae sp., Oscillospira, and Bacteroides were high in mice fed the CT diet. At the operational taxonomic unit level, Bacteroides acidifaciens- and Bacteroides caecimuris-like bacteria were highly abundant in mice fed the CT diet. Faecalibaculum rodentium- and Allobaculum stercoricanis-like bacteria were highly abundant in the mice fed the Egg diet. These sets of taxa were assumed to be estimates of casein-tallow SIBs and egg SIBs, respectively, in the gut microbiome. Among the SIBs, B. caecimuris and F. rodentium could be isolated using blood and liver agar. PRACTICAL APPLICATIONS: B. caecimuris and F. rodentium are regarded as casein-tallow and/or egg SIBs in mice. It is possible to demonstrate functionality with orally administered food ingredients. Isolation and application of human or livestock SIB is considered promising for the development of new probiotics and functional foods.

Effect of rice bran fermented with Saccharomyces cerevisiae and Lactobacillus plantarum on gut microbiome of mice fed high-sucrose diet

To clarify the effect of rice bran (RB) and fermented RB (FRB) in a high-sucrose and low-dietary fibre diet on the gut microbiome, the in vitro bile acid-lowering capacity and caecal microbiota of ICR mice fed with 20% RB or FRB diets for two weeks were determined. The caecal microbiome was analysed by 16S rRNA gene amplicon sequencing. The in vitro bile acid-lowering capacity was high for FRB. In mouse experiments, triacylglycerol and total cholesterol were generally lower with FRB, although the faecal frequency was highest in mice fed with RB. The Shannon-Wiener and Simpson's indices for alpha-diversity in the microbiome of mice fed with RB and FRB, were higher than mice fed the control diet. At the phylum level in the caecal microbiome, Firmicutes and Bacteroidetes were high with FRB and RB, respectively. At the operational taxonomic unit level, some bacterial groups related to diabetes and gut toxicity, such as Lachnospiraceae and Enterorhabdus mucosicola, were high for RB but not for FRB diets. These results suggest that FRB, rather than RB, intake improve the intestinal environment and blood lipid condition.

Change in the microbial community of saline geothermal fluids amended with a scaling inhibitor: effects of heat extraction and nitrate dosage

Geothermal plants are often affected by corrosion caused by microbial metabolites such as H₂S. In the Bad Blumau (Austria) geothermal system, an increase in microbially produced H₂S was observed in the hot (107 °C) and scaling inhibitor-amended saline fluids and in fluids that had cooled down (45 °C). Genetic fingerprinting and quantification revealed the dominance, increasing abundance and diversity of sulfate reducers such as Desulfotomaculum spp. that accompanied the cooling and processing of the geothermal fluids. In addition, a δ³⁴S isotopic signature showed the microbial origin of the H₂S that has been produced either chemolithotrophically or chemoorganotrophically. A nitrate addition test in a test pipe as a countermeasure against the microbial H₂S formation caused a shift from a biocenosis dominated by bacteria of the phylum Firmicutes to a community of Firmicutes and Proteobacteria. Nitrate supported the growth of nitrate-reducing sulfur-oxidizing Thiobacillus thioparus, which incompletely reduced nitrate to nitrite. The addition of nitrate led to a change in the composition of the sulfate-reducing community. As a result, representatives of nitrate- and nitrite-reducing SRB, such as Desulfovibrio and Desulfonatronum, emerged as additional community members. The interaction of sulfate-reducing bacteria and nitrate-reducing sulfur-oxidizing bacteria (NR-SOB) led to the removal of H₂S, but increased the corrosion rate in the test pipe.

Effect of Taurine on Intestinal Microbiota and Immune Cells in Peyer's Patches of Immunosuppressive Mice

Taurine is a sulfur-containing amino acid which has strong activities in enhancing immunity. Gut microbiota is closely interrelated with intestinal mucosal immunity, but the effects and mechanisms of taurine on intestinal microbiota and mucosal immune cells under an immunosuppressive condition remain unclear. This study was conducted to investigate the effect of taurine on gut microbiota and immune cells in Peyer's patches (PPs) of dexamethasone (Dex)-induced immunosuppressive mice. Mice (4-week-old, Male) were randomly divided into three groups: the Control group (n = 12), the Dex-induced immunosuppressive model group (n = 12) and the taurine intervention group (n = 12). The model was established by Dex injection for 7 days and the taurine intervention group was gavaged 100 mg/kg soluble taurine for 30 days. The changes of intestinal microbiota and immune cells in PPs were tested by denaturing gradient gel electrophoresis (DGGE) and flow cytometry, respectively. Results showed that the microbiota in immunosuppressive mice was obvious different compared with control group, in which, the Lachnospiraceae and Ruminococcaceae groups were significantly reduced, and their reduction were reversed after taurine intervention. Compared to the control group, the total cell number in PPs, as well as the subsets of CD3⁺ cells (T cells), CD19⁺ cells (B cells) in model groups were significantly lower, and they were dramatically improved after taurine treatment. Our results suggested that taurine has a positive effect on i ntestinal homeostasis of the immunosuppressive mice.

Obesity and mental health improvement following nutritional education focusing on gut microbiota composition in Japanese women: a randomised controlled trial

PURPOSE

Gut microbiota composition was supposedly related to obesity and psychological factors. We examined the effects of a nutritional education intervention focusing on gut microbiota composition on obesity and psychological factors among obese women.

METHODS

Forty-four obese Japanese women aged 40 or older were randomly assigned to either an intervention group (n = 22) or control group (n = 22). The intervention consisted of a 20-min dietary lecture and a 10-min counselling session by registered dieticians, every 2 weeks for eight consecutive weeks. Body weight, height, waist circumference, food frequency, and gut microbiota composition were measured, and self-rated health and psychological factors were scored before and after the intervention.

RESULTS

All participants completed the 8 week program. After the intervention, dietary fibre intake (p < 0.01), frequency of vegetable consumption (p = 0.020), and frequency of milk and milk product consumption (p < 0.01) increased significantly in the intervention group compared with the control group. Body weight and body mass index (BMI; p < 0.001), waist circumference (p < 0.01), and the depression scale score (p < 0.01) decreased significantly, while significant improvements were found in self-rated health (p = 0.045) and microbiome diversity (p < 0.01).

CONCLUSION

Nutritional education focusing on gut microbiota composition may improve obesity and psychological factors in obese women.

Lactobacillus brevis DM9218 ameliorates fructose-induced hyperuricemia through inosine degradation and manipulation of intestinal dysbiosis

OBJECTIVE

High fructose consumption exacerbates purine degradation and intestinal dysbiosis, which are closely related to the development of hyperuricemia. Probiotics are powerful weapons to combat metabolic disturbance and intestinal dysbiosis. Previously we isolated a Lactobacillus strain named DM9218 that could reduce the serum uric acid (UA) level by assimilating purine nucleosides. The present study aimed to evaluate the effects of DM9218 on high-fructose-induced hyperuricemia and to elucidate the underlying mechanisms.

METHODS

Mice were fed a normal diet, a high-fructose diet, or high-fructose diet with DM9218. Metabolic parameters, fructose- and UA-related metabolites, and fecal microbiota were investigated. Whole-genome sequencing of strain DM9218 was also conducted. In addition, an inosine hydrolase from DM9218 was heterologously expressed in Escherichia coli, and its inosine-degrading activity was detected.

RESULTS

Our results indicated that DM9218 could decrease serum UA level and hepatic xanthine oxidase activity in fructose-fed mice. It could protect against high-fructose-induced liver damage and retard UA accumulation by degrading inosine. The modulation effect of DM9218 on high-fructose-induced intestinal dysbiosis resulted in enhancement of intestinal barrier function and reduction of liver lipopolysaccharide, which was closely correlated with the down-regulation of inflammatory cytokine-stimulated xanthine oxidase expression and activity.

CONCLUSIONS

Lactobacillus brevis DM9218 is a probiotic strain with the potential to ameliorate fructose-induced hyperuricemia.

Dynamic changes of bacterial communities and nitrite character during northeastern Chinese sauerkraut fermentation

Northeastern Chinese sauerkraut is a well-known traditional fermented vegetable in China. Incomplete identification of the microorganisms' (bacteria in spontaneous fermentation) diversity and accumulation of nitrite make it difficult to normalize the fermentation process and product qualities of northeastern Chinese sauerkraut. Conventional culturing and polymerase chain reaction-denaturing gradient gel electrophoresis methods were combined to describe microbial structure and diversity. Lactobacillus, Leuconostoc, Enterobacter, Accumulibacter, Thermotoga, Pseudomonas, Clostridium, Rahnella and Citrobacter were predominant microorganisms in different fermentation periods. The pH value and nitrite concentration presented a certain relevance to the amount of lactic acid bacteria. Lactobacillus and Leuconostoc had the ability to decrease nitrite by inhibiting nitrate-reducing bacteria such as Enterobacter. Therefore, Northeastern Chinese sauerkraut should not be eaten until 4 weeks of fermentation for the safety and quality of fermented foods. Northeastern Chinese sauerkraut is rich in lactic acid bacteria, which demonstrate its ability as an excellent probiotic for applications in functional foods.

Bacterial Diversity in Traditional Doogh in Comparison to Industrial Doogh

Forty-four samples of traditional Doogh and yoghurt were collected from 13 regions of 4 provinces in west of Iran (13 area) and analyzed using molecular methods including PCR, denaturing gradient gel electrophoresis (DGGE) of 16S rDNA, and sequencing. Moreover, collected samples as well as samples from industrially Doogh were analyzed with quantitative real-time PCR (RT-PCR). Analyzed 16S rRNA gene sequences of Doogh samples could be allocated to the presence of Lactobacillus spp. The typical yoghurt starter culture bacteria included four different Lactobacillus species with possible probiotic properties, L. acidophilus, L. helveticus, L. kefiranofaciens, and L. amylovorus. DGGE of traditional Doogh and yoghurt and RT-PCR of traditional Doogh and yoghurt and also industrial Doogh samples demonstrated that traditional Doogh and yoghurt show a higher abundance of total bacteria and lactobacilli and a higher bacterial diversity, respectively. Considering diversity and higher probiotic bacteria content in traditional Doogh, consumers’ healthiness in tribes and villages could be promoted with these indigenous products.

Biodegradation of tetrabromobisphenol A in the sewage sludge process

Anaerobic sewage sludge capable of rapidly degrading tetrabromobisphenol A (TBBPA) was successfully acclimated in an anaerobic reactor over 280days. During the period from 0 to 280days, the TBBPA degradation rate (DR), utilization of glucose, and VSS were monitored continuously. After 280days of acclimation, the TBBPA DR of active sludge reached 96.0% after 20days of treatment in batch experiments. Based on scanning electron microscopy (SEM) observations and denaturing gradient gel electrophoresis (DGGE) determinations, the diversity of the microorganisms after 0 and 280days in the acclimated anaerobic sewage sludge was compared. Furthermore, eleven metabolites, including 2-bromophenol, 3-bromophenol, 2,4-dibromophenol, 2,6-dibromophenol, tribromophenol and bisphenol A, were identified by gas chromatography-mass spectrometry (GC-MS). Moreover, the six primary intermediary metabolites were also well-degraded by the acclimated anaerobic sewage sludge to varying degrees. Among the six target metabolites, tribromophenol was the most preferred substrate for biodegradation via debromination. These metabolites degraded more rapidly than monobromide and bisphenol A. The biodegradation data of the intermediary metabolites exhibited a good fit to a pseudo-first-order model. Finally, based on the metabolites, metabolic pathways were proposed. In conclusion, the acclimated microbial consortia degraded TBBPA and its metabolites well under anaerobic conditions.

Effects of toxic organic flotation reagent (aniline aerofloat) on an A/O submerged membrane bioreactor (sMBR): Microbial community dynamics and performance

Bio-treatment of flotation wastewater has been proven to be both effective and economical, as a treatment method. Despite this, little is known regarding the effects of toxic organic floatation reagents such as Dianilinodithiophosphoric acid (DDA), on the microbial community performance or dynamics, which are critical to the effective performance of the bio-treatment reactor. A submerged membrane bioreactor (sMBR) was constructed to continuously treat simulated wastewater contaminated with DDA, an organic flotation reagent that is now considered a significant pollutant. The performance of the sMBR system was investigated at different DDA loading concentrations, with assessment of the effects of DDA on the microbial communities within the sMBR, in particular the biodiversity and succession within the microbial community. Results showed that, with increased DDA loadings, the performance of the sMBR was initially negatively affected, but the system adapted efficiently and consistently reached a COD removal rate of up to 80%. Increased DDA loading concentrations had an adverse effect on the activity of both the activated sludge and microbial communities, resulting in a large alteration in microbial dynamics, especially during the start-up stage and the high DDA loading stage. Strains capable of adapting to the presence of DDA, capable of degrading DDA or utilizing its byproducts, were enriched within the sMBR community, such as Zoogloea, Clostridium, Sideroxydans lithotrophicus, Thiobacillus, Thauera amino aromatica and Alicycliphilus denitrificans.

Impact of whey proteins on the systemic and local intestinal level of mice with diet induced obesity

Obesity is a serious public health problem and being multifactorial is difficult to tackle. Since the intestinal ecosystem's homeostasis is, at least partially, diet-dependent, its modulation may be triggered by food components that are designed to exert a modulatory action leading to a health-promoting effect. Milk whey proteins, are considered as such promising factors since they influence satiation as well as body weight and constitute the source of biologically active peptides which may modulate health status locally and systemically. This way, whey proteins are associated with obesity. Therefore, this paper is aimed at the estimation of the impact of whey proteins using a commercially available whey protein isolate on the physiological response of mice with diet-induced obesity. The physiological response was evaluated on the local-intestinal level, scrutinizing intestinal microbiota as one of the important factors in obesity and on the systemic level, analyzing the response of the organism. Whey proteins brought about the decrease of the fat mass with a simultaneous increase of the lean mass of animals with diet induced obesity, which is a promising, health-promoting effect. Whey proteins also proved to act beneficially helping restore the number of beneficial bifidobacteria in obese animals and decreasing the calorie intake and fat mass as well as the LDL level. Overall, supplementation of the high fat diet with whey proteins acted locally by restoration of the intestinal ecosystem, thus preventing dysbiosis and its effects and also acted systemically by strengthening the organism increasing the lean mass and thus hindering obesity-related detrimental effects.

Molecular Study of Indigenous Bacterial Community Composition on Exposure to Soil Arsenic Concentration Gradient

Community structure of bacteria present in arsenic contaminated agricultural soil was studied with qPCR (quantitative PCR) and DGGE (Denaturing Gradient Gel Electrophoresis) as an indicator of extreme stresses. Copy number of six common bacterial taxa (Acidobacteria, Actinobacteria, α-, β- and γ-Proteobacteria, Firmicutes) was calculated using group specific primers of 16S rDNA. It revealed that soil contaminated with low concentration of arsenic was dominated by both Actinobacteria and Proteobacteria but a shift towards Proteobacteria was observed with increasing arsenic concentration, and number of Actinobacteria eventually decreases. PCA (Principle Component Analysis) plot of bacterial community composition indicated a distinct resemblance among high arsenic content samples, while low arsenic content samples remained separated from others. Cluster analysis of soil parameters identifies three clusters, each of them was related to the arsenic content. Further, cluster analysis of 16S rDNA based DGGE fingerprint markedly distributed the soil bacterial populations into low (< 10 ppm) and high (> 10 ppm) arsenic content subgroups. Following analysis of diversity indices shows significant variation in bacterial community structure. MDS (Multi Dimensional Scaling) plot revealed distinction in the distribution of each sample denoting variation in bacterial diversity. Phylogenetic sequence analysis of fragments excised from DGGE gel revealed the presence of γ-Proteobacteria group across the study sites. Collectively, our experiments indicated that gradient of arsenic contamination affected the shape of the soil bacterial population by significant structural shift.

Metagenomic analyses of bacterial endophytes associated with the phyllosphere of a Bt maize cultivar and its isogenic parental line from South Africa

Genetic modification of maize with Bacillus thuringiensis (Bt) cry proteins may predispose shifts in the bacterial endophytes' community associated with maize shoots. In this study, the diversity of bacterial endophytes associated with a Bt maize genotype (Mon810) and its isogenic non-transgenic parental line were investigated at pre-flowering (50 days) and post-flowering (90 days) developmental stages. PCR-DGGE and high throughput sequencing on the Illumina MiSeq sequencer were used to characterize bacterial 16S rRNA gene diversity in leaves, stems, seeds and tassels. PCR-DGGE profile revealed similarity as well as differences between bacterial communities of shoots in both cultivars and at both developmental stages. A total of 1771 operational taxonomic units (OTUs) were obtained from the MiSeq and assigned into 14 phyla, 27 classes, 58 orders, 116 families and 247 genera. Differences in alpha and beta diversity measures of OTUs between the phyllospheres of both genotypes were not significant (P > .05) at all developmental stages. In all cultivars, OTU diversity reduced with plant development. OTUs belonging to the phyla Proteobacteria were dominant in all maize phyllospheres. The class Gammaproteobacteria was dominant in Bt maize while, Alphaproteobacteria and Actinobacteria were dominant in non-Bt maize phyllospheres. Differences in the abundance of some genera, including Acidovorax, Burkerholderia, Brachybacterium, Enterobacter and Rhodococcus, whose species are known beneficial endophytes were observed between cultivars. Hierarchical cluster analysis further suggests that the bacterial endophyte communities of both maize genotypes associate differently (are dissimilar). Overall, the results suggest that bacterial endophytes community differed more across developmental stages than between maize genotypes.

Diazinon dissipation in pesticide-contaminated paddy soil: kinetic modeling and isolation of a degrading mixed bacterial culture

Dissipation kinetics of diazinon was investigated in soils culled from a paddy field with a long history of the pesticide application. Goodness of fit statistical indices derived from several fitted mono- and bi-exponential kinetic models revealed a bi-phasic pattern of the diazinon dissipation curve at 15 and 150 mg kg^-1 spiking levels, which could be described best by the first-order double exponential decay (FODED) model. Parameters obtained from this model were able to describe the enhanced dissipation of diazinon as the result of repeated soil applications, where a larger fraction of the pesticide readily available in the solution phase was dissipated with a fast rate. Cluster and principal component analysis (PCA) of denaturing gradient gel electrophoresis (DGGE) obtained from soil bacterial populations revealed that they were only affected at the 150 mg kg^-1 diazinon concentration. This was also supported by the phylogenetic tree obtained from sequences of the main gel bands. Accordingly, bacterial populations belonging to Proteobacteria were enriched in the soil following three treatments with diazinon at 150 mg kg^-1. The Shannon's index revealed a nonsignificant increase (P ≤ 0.05) in overall diversity of soil bacteria following diazinon application. Diazinon-degrading bacteria were isolated from the paddy soils in a mineral salt medium. Results showed that the isolated mixed culture was able to remove 90% of the pesticide at two concentrations of 50 and 100 mg L^-1 by 16.81 and 19.60 days, respectively. Sequencing the DGGE bands confirmed the role of Betaproteobacteria as the main components of the isolated mixed culture in the degradation of diazinon.

Diversity of the Bacterial Microbiota of Anopheles Mosquitoes from Binh Phuoc Province, Vietnam

The naturally acquired microbiota of Anopheles can influence vector’s susceptibility to Plasmodium and its capacity to transmit them. Microbiota modification is a new challenge to limit disease transmission but it still needs advanced knowledges on bacterial community in Anopheles, especially in wild and infected specimens from diverse origin and species. Bacterial culture and 16S rRNA gene-PCR associated to Temporal Temperature Gradient Electrophoresis (TTGE) were applied to explore the bacterial diversity in the abdomen of 100 wild specimens (eight Anopheles species) collected in the Binh Phuoc Province, Vietnam. Culture and PCR-TTGE were complementary. The bacterial richness of the mosquito collection encompassed 105 genera belonging to seven phyla, mostly Proteobacteria, Firmicutes, and Actinobacteria. Staphylococcus, Clostridium, and Bacillus in Firmicutes were the most prevalent genera. However, Proteobacteria represented by 57 genera was the most diversified phylum in Anopheles microbiota. The high overall of Anopheles-associated bacteria is confirmed with, to our knowledge, 51 genera described for the first time in Anopheles microbiota. However, the diversity per specimen was low with average diversity index and the average Shannon–Wiener score (H) of 4.843 and 5.569, respectively. The most represented bacterial genera were present in <30% of the specimens. Consequently, the core microbiota share by Anopheles from Binh Phuoc was very narrow, suggesting that Anopheles microbiota was greatly influenced by local environments. The repertory of bacterial genera in two specimens of An. dirus and An. pampanai naturally infected by Plasmodium vivax was also described as preliminary results. Finally, this study completed the repertory of bacteria associated to wild Anopheles. Anopheles associated-bacteria appeared specimen-dependent rather than mosquitoe species- or group-dependent. Their origin and the existence of Anopheles-specific bacterial taxa are discussed.

Effects of Maydis stigma polysaccharide on the intestinal microflora in type-2 diabetes

CONTEXT

Diabetes is a serious endocrine and metabolic disorder. Food supplements attract people's attention in mitigating health problems from the aspect of gastrointestinal microflora. Maydis stigma (Zea mays subsp. mays L. [Poaceae]), has been used as water decoction for treating diabetes in folk medicine. It has great potential, and feasibly a stable form of Maydis stigma commercial products could be developed to fulfil the health food market.

OBJECTIVE

To study the effects of Maydis stigma polysaccharide (MSP) on the intestinal microflora in type-2 diabetes (T2D).

MATERIALS AND METHODS

MSP was fractioned from Maydis stigma by distilled water, purified by DEAE-52 Cellulose chromatography and Sephadex G-200 gel column. Streptozotocin (160 mg/kg) was intraperitoneal injected for 3 days to build model. The diabetic mice were randomly divided into five groups together with control group (10 mice in each group). The doses of MSP were 400, 600 and 800 mg/kg, respectively. After 5 weeks of administration, antidiabetic effects and intestinal microflora balance restoring activities were evaluated by denaturing gradient gel electrophoresis.

RESULTS

Blood glucose levels of MSP-treated groups showed extremely significant hypoglycemic effects (p < 0.01), body weight increased showed extremely significant (p < 0.01) differences. Bacteroides, Lactobacillus and Prevotella were dominant organisms in the intestinal tract. The quality and quantity of Lactobacillus and Bacteroides genus increased remarkably with increasing concentration of MSP.

DISCUSSION AND CONCLUSION

Experimental results of this study suggest that MSP has the significant potential to be used as a natural agent for treating T2D and restoring the intestinal microflora balance.

Edible Safety Assessment of Genetically Modified Rice T1C-1 for Sprague Dawley Rats through Horizontal Gene Transfer, Allergenicity and Intestinal Microbiota

In this study, assessment of the safety of transgenic rice T1C-1 expressing Cry1C was carried out by: (1) studying horizontal gene transfer (HGT) in Sprague Dawley rats fed transgenic rice for 90 d; (2) examining the effect of Cry1C protein in vitro on digestibility and allergenicity; and (3) studying the changes of intestinal microbiota in rats fed with transgenic rice T1C-1 in acute and subchronic toxicity tests. Sprague Dawley rats were fed a diet containing either 60% GM Bacillus thuringiensis (Bt) rice T1C-1 expressing Cry1C protein, the parental rice Minghui 63, or a basic diet for 90 d. The GM Bt rice T1C-1 showed no evidence of HGT between rats and transgenic rice. Sequence searching of the Cry1C protein showed no homology with known allergens or toxins. Cry1C protein was rapidly degraded in vitro with simulated gastric and intestinal fluids. The expressed Cry1C protein did not induce high levels of specific IgG and IgE antibodies in rats. The intestinal microbiota of rats fed T1C-1 was also analyzed in acute and subchronic toxicity tests by DGGE. Cluster analysis of DGGE profiles revealed significant individual differences in the rats' intestinal microbiota.

Administration of probiotic mixture DM#1 ameliorated 5-fluorouracil-induced intestinal mucositis and dysbiosis in rats

OBJECTIVE

The use of probiotics to alleviate chemotherapy-induced intestinal mucositis is supported by clinical consensus. However, no studies to date, to our knowledge, have systematically analyzed the effects of a probiotic mixture on chemotherapy-induced mucositis or assessed changes in the intestinal microbiota after probiotic treatment. The aim of this study was to report the effects of a probiotic mixture, DM#1, on intestinal mucositis and dysbiosis of rats treated with 5-fluorouracil (5-FU).

METHODS

Twenty-eight male Sprague Dawley rats weighing 180 to 220 g were randomly divided into four groups: control, 5-FU, probiotic high (PH), and probiotic low (PL). Except for the control group, all other groups received intraperitoneal injections of 5-FU for 5 d, and the PH and PL groups received DM#1 intragastrically (1 × 10⁹ or 1 × 10⁸ colony-forming units/kg, respectively) for 8 d. One day after the last administration, rats were sacrificed and the ilea were removed for histopathologic assessment and evaluation of permeability, myeloperoxidase activity, levels of cytokines (interleukin [IL]-4, IL-6, tumor necrosis factor [TNF]-α), and mRNA of toll-like receptors (TLR; TLR2, TLR4, and TLR9). Additionally, intestinal microbiota profiles were analyzed by polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis and quantitative real-time PCR.

RESULTS

Treatment with DM#1 ameliorated 5-FU-induced intestinal mucosal injury in rats, possibly by reducing proinflammatory cytokine levels and neutrophil infiltration. The increased intestinal permeability caused by 5-FU was ameliorated. These results were closely associated with the reestablishment of intestinal microbial homeostasis and alteration of the TLR2/TLR4 signaling pathway.

CONCLUSIONS

Administration of the probiotic mixture DM#1 ameliorated 5-FU-induced intestinal mucositis and dysbiosis in rats.

Proteobacteria from the human skin microbiota: Species-level diversity and hypotheses

The human skin microbiota is quantitatively dominated by Gram-positive bacteria, detected by both culture and metagenomics. However, metagenomics revealed a huge variety of Gram-negative taxa generally considered from environmental origin. For species affiliation of bacteria in skin microbiota, clones of 16S rRNA gene and colonies growing on diverse culture media were analyzed. Species-level identification was achieved for 81% of both clones and colonies. Fifty species distributed in 26 genera were identified by culture, mostly belonging to Actinobacteria and Firmicutes, while 45 species-level operational taxonomic units distributed in 30 genera were detected by sequencing, with a high diversity of Proteobacteria. This mixed approach allowed the detection of 100% of the genera forming the known core skin Gram-negative microbiota and 43% of the known diversity of Gram-negative genera in human skin. The orphan genera represented 50% of the current skin pan-microbiota. Improved culture conditions allowed the isolation of Roseomonas mucosa, Aurantimonas altamirensis and Agrobacterium tumefaciens strains from healthy skin. For proteobacterial species previously described in the environment, we proposed the existence of skin-specific ecotypes, which might play a role in the fine-tuning of skin homeostasis and opportunistic infections but also act as a shuttle between environmental and human microbial communities. Therefore, skin-associated proteobacteria deserve to be considered in the One-Health concept connecting human health to the health of animals and the environment.

Survival of Lactobacillus casei strain Shirota in the intestines of healthy Chinese adults

Lactobacillus casei strain Shirota (LcS) is a widely used probiotic strain with health benefits. In this study, the survival of LcS in the intestines of healthy Chinese adults was assessed and the effects of LcS on stool consistency, stool SCFAs and intestinal microbiota evaluated. Subjects consumed 100 mL per day of a probiotic beverage containing 1.0 × 10(8) CFU/mL of LcS for 14 days. LcS were enumerated using a culture method and the colony identity confirmed by ELISA. Fourteen days after ingestion, the amount of LcS recovered from fecal samples was between 6.86 ± 0.80 and 7.17 ± 0.57 Log10 CFU/g of feces (mean ± SD). The intestinal microbiotas were analyzed by denaturing gradient gel electrophoresis. Principal component analysis showed that consuming LcS significantly changed fecal microbiota profiles. According to redundancy analysis, the amounts of 25 bacterial strains were significantly correlated with LcS intake (P < 0.05), 11 of them positively and fourteen negatively. Concentrations of acetic acid and propionic acid in feces were significantly lower during the ingestion period than during the baseline period (P < 0.05). These results confirm that LcS can survive passage through the gastrointestinal tract of Chinese people; however, they were found to have little ability to persist once their consumption had ceased. Furthermore, consumption of probiotic beverages containing LcS can modulate the composition of the intestinal microbiota on a long-term basis, resulting in decreased concentrations of SCFAs in the gut.

Diversity of the Bacterial Microbiota of Anopheles Mosquitoes from Binh Phuoc Province, Vietnam

The naturally acquired microbiota of Anopheles can influence vector's susceptibility to Plasmodium and its capacity to transmit them. Microbiota modification is a new challenge to limit disease transmission but it still needs advanced knowledges on bacterial community in Anopheles, especially in wild and infected specimens from diverse origin and species. Bacterial culture and 16S rRNA gene-PCR associated to Temporal Temperature Gradient Electrophoresis (TTGE) were applied to explore the bacterial diversity in the abdomen of 100 wild specimens (eight Anopheles species) collected in the Binh Phuoc Province, Vietnam. Culture and PCR-TTGE were complementary. The bacterial richness of the mosquito collection encompassed 105 genera belonging to seven phyla, mostly Proteobacteria, Firmicutes, and Actinobacteria. Staphylococcus, Clostridium, and Bacillus in Firmicutes were the most prevalent genera. However, Proteobacteria represented by 57 genera was the most diversified phylum in Anopheles microbiota. The high overall of Anopheles-associated bacteria is confirmed with, to our knowledge, 51 genera described for the first time in Anopheles microbiota. However, the diversity per specimen was low with average diversity index and the average Shannon-Wiener score (H) of 4.843 and 5.569, respectively. The most represented bacterial genera were present in <30% of the specimens. Consequently, the core microbiota share by Anopheles from Binh Phuoc was very narrow, suggesting that Anopheles microbiota was greatly influenced by local environments. The repertory of bacterial genera in two specimens of An. dirus and An. pampanai naturally infected by Plasmodium vivax was also described as preliminary results. Finally, this study completed the repertory of bacteria associated to wild Anopheles. Anopheles associated-bacteria appeared specimen-dependent rather than mosquitoe species- or group-dependent. Their origin and the existence of Anopheles-specific bacterial taxa are discussed.

Responses of soil fungal community to the sandy grassland restoration in Horqin Sandy Land, northern China

Sandy grassland restoration is a vital process including re-structure of soils, restoration of vegetation, and soil functioning in arid and semi-arid regions. Soil fungal community is a complex and critical component of soil functioning and ecological balance due to its roles in organic matter decomposition and nutrient cycling following sandy grassland restoration. In this study, soil fungal community and its relationship with environmental factors were examined along a habitat gradient of sandy grassland restoration: mobile dunes (MD), semi-fixed dunes (SFD), fixed dunes (FD), and grassland (G). It was found that species abundance, richness, and diversity of fungal community increased along with the sandy grassland restoration. The sequences analysis suggested that most of the fungal species (68.4 %) belonged to the phylum of Ascomycota. The three predominant fungal species were Pleospora herbarum, Wickerhamomyces anomalus, and Deconica Montana, accounting for more than one fourth of all the 38 species. Geranomyces variabilis was the subdominant species in MD, Pseudogymnoascus destructans and Mortierella alpine were the subdominant species in SFD, and P. destructans and Fungi incertae sedis were the dominant species in FD and G. The result from redundancy analysis (RDA) and stepwise regression analysis indicated that the vegetation characteristics and soil properties explain a significant proportion of the variation in the fungal community, and aboveground biomass and C:N ratio are the key factors to determine soil fungal community composition during sandy grassland restoration. It was suggested that the restoration of sandy grassland combined with vegetation and soil properties improved the soil fungal diversity. Also, the dominant species was found to be alternative following the restoration of sandy grassland ecosystems.

Effect of Elevated Atmospheric CO2 and Temperature on the Disease Severity of Rocket Plants Caused by Fusarium Wilt under Phytotron Conditions

The severity of F. oxysporum f.sp. conglutinans on rocket plants grown under simulated climate change conditions has been studied. The rocket plants were cultivated on an infested substrate (4 log CFU g-1) and a non-infested substrate over three cycles. Pots were placed in six phytotrons in order to simulate different environmental conditions: 1) 400-450 ppm CO2, 18-22°C; 2) 800-850 ppm CO2, 18-22°C; 3) 400-450 ppm CO2, 22-26°C, 4) 800-850 ppm CO2, 22-26°C, 5) 400-450 ppm CO2, 26-30°C; 6) 800-850 ppm CO2, 26-30°C. Substrates from the infested and control samples were collected from each phytotron at 0, 60 and 120 days after transplanting. The disease index, microbial abundance, leaf physiological performances, root exudates and variability in the fungal profiles were monitored. The disease index was found to be significantly influenced by higher levels of temperature and CO2. Plate counts showed that fungal and bacterial development was not affected by the different CO2 and temperature levels, but a significant decreasing trend was observed from 0 up to 120 days. Conversely, the F. oxysporum f.sp. conglutinans plate counts did not show any significantly decrease from 0 up to 120 days. The fungal profiles, evaluated by means of polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE), showed a relationship to temperature and CO2 on fungal diversity profiles. Different exudation patterns were observed when the controls and infested plants were compared, and it was found that both CO2 and temperature can influence the release of compounds from the roots of rocket plants. In short, the results show that global climate changes could influence disease incidence, probably through plant-mediated effects, caused by soilborne pathogens.

Bacterial analysis of combined periodontal-endodontic lesions by polymerase chain reaction-denaturing gradient gel electrophoresis

We used denaturing gradient gel electrophoresis (DGGE) to compare bacterial profiles in periodontium and root canals of teeth with combined periodontal-endodontic lesions. Samples of dental plaque and necrotic pulp were collected from thirteen extracted teeth with advanced periodontitis. Genomic DNA was extracted for polymerase chain reaction (PCR) analysis using universal bacterial primers. The PCR products were then loaded onto DGGE gels to obtain fractionated bands. Characteristic DGGE bands were excised and DNA was cloned and sequenced. The number of bands, which indicates the number of bacterial species, was compared between dental plaques and necrotic pulp tissues from the same tooth. Although the difference was statistically significant (P < 0.01), there was no positive correlation; similarity (Dice coefficient) was 13.1% to 62.5%. Some bacteria species were present in both the periodontal pockets and root canals of the same tooth; however, periodontal bacteria did not always invade the root canals, and some bacteria in root canals were not present in periodontal pockets of the same tooth. In some teeth, unique bacteria in root canals had not passed from periodontal pockets. A basic local alignment search tool (BLAST) sequence search in Genbank indicated that new bacteria species were present in periodontal pockets and root canals. Their characteristics must thus be further analyzed.

Comparison of the gut microbiota composition between obese and non-obese individuals in a Japanese population, as analyzed by terminal restriction fragment length polymorphism and next-generation sequencing

BACKGROUND

Obesity has become one of the most serious social problems in developed countries, including Japan. The relationship between the gut microbiota and obesity has recently attracted the attention of many researchers. Although the gut microbiota was long thought to contribute to obesity, the exact association remains largely unknown. We examined the human gut microbiota composition in a Japanese population in order to determine its relationship to obesity.

METHODS

Stool samples from 23 non-obese subjects (body mass index [BMI] <20 kg/m(2)) and 33 obese subjects (BMI ≥25 kg/m(2)) were collected and DNA was extracted prior to colonoscopy. After terminal restriction fragment length polymorphism (T-RFLP) analysis, samples from 10 subjects (4 non-obese and 6 obese) were selected and subjected to next-generation sequencing for species-level analysis.

RESULTS

T-RFLP analysis showed significantly reduced numbers of Bacteroidetes and a higher Firmicutes to Bacteroidetes ratio in obese subjects compared with non-obese subjects. Bacterial diversity was significantly greater in obese subjects compared with non-obese subjects. Next-generation sequencing revealed that obese and non-obese subjects had different gut microbiota compositions and that certain bacterial species were significantly associated with each group (obese: Blautia hydrogenotorophica, Coprococcus catus, Eubacterium ventriosum, Ruminococcus bromii, Ruminococcus obeum; non-obese: Bacteroides faecichinchillae, Bacteroides thetaiotaomicron, Blautia wexlerae, Clostridium bolteae, Flavonifractor plautii).

CONCLUSION

Gut microbial properties differ between obese and non-obese subjects in Japan, suggesting that gut microbiota composition is related to obesity.

Effects of glucose on microcystin-LR removal and the bacterial community composition through anoxic biodegradation in drinking water sludge

To enhance the degradation efficiency of microcystin (MC) in drinking water sludge (DWS), the underlying mechanisms between organic carbon (glucose) and the biodegradation of MC-LR under anoxic conditions were investigated by polymerase chain reaction-denaturing gradient gel electrophoresis technology. The addition of glucose reduced the rate of the MC-LR biodegradation indicating the occurrence of inhibition of degradation, and an increased inhibition was observed with increases in glucose concentration (0-10,000 mg/L). In addition, the community analysis indicated that the variety and the number of the microbes increased with the concentration of glucose amended (0 -1000 mg/L), but they decreased substantially with the addition of 10,000 mg/L of glucose. The phyla Firmicutes, Proteobacteria and Chloroflexi were found to be the dominant. Methylobacterium and Sphingomonas were MC-degrading bacteria and used glucose as a prior carbon source instead of MC, resulting in the decrease in the MC-LR biodegradation rate under anoxic conditions. Thus, reducing organic carbon could improve the anoxic biodegradation efficiency of MC in DWS.

Profiling of Oral and Nasal Microbiome in Children With Cleft Palate

OBJECTIVE

To identify the oral and nasal microbial profile of cleft palate children and control children and to reveal interrelationships between the microbiome and the high prevalence of infectious diseases.

DESIGN

Saliva and nasal samples of 10 cleft palate children and 10 age-matched control children were analyzed. Total microbial genomic DNA was isolated, polymerase chain reaction-denaturing gradient gel electrophoresis was applied to obtain fingerprints, and selected bands on fingerprints were sequenced.

RESULTS

The results revealed a significantly lower saliva microbial diversity in cleft children and a different microbial component in both saliva and nares in children with cleft palate. A higher component similarity between the oral and nasal samples was found in the cleft group than in the control group. Lautropia species and Bacillus species were significantly less present among the saliva samples of cleft group. Dolosigranulum species and Bacillus species were significantly fewer in the nasal cavity of cleft group. Streptococcus species became much more predominant in the nasal cavity of the cleft group than in that of the control group.

CONCLUSIONS

A disturbed ecological ecosystem is found in oral and nasal microbiome of children with cleft palate as a consequence of the abnormal communication between the two cavities. Further studies are needed to explore the relationship between the disturbed microbiome and diseases.

Fecal Microbiota in Healthy Subjects Following Omnivore, Vegetarian and Vegan Diets: Culturable Populations and rRNA DGGE Profiling

In this study, the fecal microbiota of 153 healthy volunteers, recruited from four different locations in Italy, has been studied by coupling viable counts, on different microbiological media, with ribosomal RNA Denaturing Gradient Gel Electrophoresis (rRNA-DGGE). The volunteers followed three different diets, namely omnivore, ovo-lacto-vegetarian and vegan. The results obtained from culture-dependent and -independent methods have underlined a high level of similarity of the viable fecal microbiota for the three investigated diets. The rRNA DGGE profiles were very complex and comprised a total number of bands that varied from 67 to 64 for the V3 and V9 regions of the 16S rRNA gene, respectively. Only a few bands were specific in/of all three diets, and the presence of common taxa associated with the dietary habits was found. As far as the viable counts are concerned, the high similarity of the fecal microbiota was once again confirmed, with only a few of the investigated groups showing significant differences. Interestingly, the samples grouped differently, according to the recruitment site, thus highlighting a higher impact of the food consumed by the volunteers in the specific geographical locations than that of the type of diet. Lastly, it should be mentioned that the fecal microbiota DGGE profiles obtained from the DNA were clearly separated from those produced using RNA, thus underlining a difference between the total and viable populations in the fecal samples.

Habitat Fragmentation can Modulate Drought Effects on the Plant-soil-microbial System in Mediterranean Holm Oak (Quercus ilex) Forests

Ecological transformations derived from habitat fragmentation have led to increased threats to above-ground biodiversity. However, the impacts of forest fragmentation on soils and their microbial communities are not well understood. We examined the effects of contrasting fragment sizes on the structure and functioning of soil microbial communities from holm oak forest patches in two bioclimatically different regions of Spain. We used a microcosm approach to simulate the annual summer drought cycle and first autumn rainfall (rewetting), evaluating the functional response of a plant-soil-microbial system. Forest fragment size had a significant effect on physicochemical characteristics and microbial functioning of soils, although the diversity and structure of microbial communities were not affected. The response of our plant-soil-microbial systems to drought was strongly modulated by the bioclimatic conditions and the fragment size from where the soils were obtained. Decreasing fragment size modulated the effects of drought by improving local environmental conditions with higher water and nutrient availability. However, this modulation was stronger for plant-soil-microbial systems built with soils from the northern region (colder and wetter) than for those built with soils from the southern region (warmer and drier) suggesting that the responsiveness of the soil-plant-microbial system to habitat fragmentation was strongly dependent on both the physicochemical characteristics of soils and the historical adaptation of soil microbial communities to specific bioclimatic conditions. This interaction challenges our understanding of future global change scenarios in Mediterranean ecosystems involving drier conditions and increased frequency of forest fragmentation.

Investigation of salivary function and oral microbiota of radiation caries-free people with nasopharyngeal carcinoma

Radiation caries have been reported to be correlated with radiotherapy-induced destruction of salivary function and changes in oral microbiota. There have been no published reports detailing patients who have remained radiation caries-free following radiotherapy for nasopharyngeal carcinoma. The aim of this study was to investigate the relationship between salivary function, oral microbiota and the absence of radiation caries. Twelve radiation caries-free patients and nine patients exhibiting radiation caries following irradiated nasopharyngeal carcinoma were selected. V40, the dose at which the volume of the contralateral parotid gland receives more than 40 Gy, was recorded. Stimulated saliva flow rate, pH values and buffering capacity were examined to assess salivary function. Stimulated saliva was used for molecular profiling by Denaturing Gradient Gel Electrophoresis. Mutans streptococci and Lactobacilli in saliva were also cultivated. There were no significant differences in V40 between radiation caries-free individuals and those with radiation caries. Compared with normal values, the radiation caries-free group had significantly decreased simulated saliva flow rate, while there were no significant differences in the saliva pH value and buffering capacity. Similar results were observed in the radiation caries group. There was no statistical difference in microbial diversity, composition and log CFU counts in cultivation from the radiation caries-free group and the radiation caries group. Eleven genera were detected in these two groups, among which Streptococcus spp. and Neisseria spp. had the highest distribution. Our results suggest that changes in salivary function and in salivary microbiota do not explain the absence of radiation caries in radiation caries-free individuals.

Biological sulphide removal from anaerobically treated domestic sewage: reactor performance and microbial community dynamics

We developed a biological sulphide oxidation system and evaluated two reactors (shaped similar to the settler compartment of an up-flow anaerobic sludge blanket [UASB] reactor) with different support materials for biomass retention: polypropylene rings and polyurethane foam. The start-up reaction was achieved using microorganisms naturally occurring on the open surface of UASB reactors treating domestic wastewater. Sulphide removal efficiencies of 65% and 90% were achieved with hydraulic retention times (HRTs) of 24 and 12 h, respectively, in both reactors. However, a higher amount of elemental sulphur was formed and accumulated in the biomass from reactor 1 (20 mg S(0) g(-1) VTS) than in that from reactor 2 (2.9 mg S(0) g(-1) VTS) with an HRT of 24 h. Denaturing gradient gel electrophoresis (DGGE) results revealed that the the pink and green biomass that developed in both reactors comprised a diverse bacterial community and had sequences related to phototrophic green and purple-sulphur bacteria such as Chlorobium sp., Chloronema giganteum, and Chromatiaceae. DGGE band patterns also demonstrated that bacterial community was dynamic over time within the same reactor and that different support materials selected for distinct bacterial communities. Taken together, these results indicated that sulphide concentrations of 1-6 mg L(-1) could be efficiently removed from the effluent of a pilot-scale UASB reactor in two sulphide biological oxidation reactors at HRTs of 12 and 24 h, showing the potential for sulphur recovery from anaerobically treated domestic wastewater.

Intestinal microbiota succession and immunomodulatory consequences after introduction of Lactobacillus reuteri I5007 in neonatal piglets

Seventy-two, suckling piglets, obtained from 9 litters standardized to 8 piglets, were assigned to 1 of 3 treatments (n = 24) to compare short-term, early administration with intermittent, longer-term administration of Lactobacillus reuteri I5007. The treatments were a control (given a placebo of 0.1% peptone water from day 1 to 5) or treatments in which 1.7 × 10¹⁰ CFU L. reuteri was administrated either daily for 4 days starting on day 1 or every 4th day from day 1 to 17. Five piglets per treatment were killed at 3 time points (day 7, 14 and 21). Denaturing Gradient Electrophoresis of ileal digesta revealed an increase in the presence of L. reuteri I5007 and Clostridium lentocellum (on day 14 and 21) in the every 4th-day treatment and Actinobacillus porcinus (on day 7 and 14) in both L. reuteri treatments, while reducing the abundance of E. coli on day 21 in the every 4th-day treatment. Real-time qPCR of ileal digesta showed an increase in Bifidobacterium spp. on day 14 for both L. reuteri I5007 treatments. An increase in the concentration of lactic acid and a lower pH was observed in the first 4-day treatment on day 7 and the every 4^th day treatment on day 14. The relative abundance of mRNA for TGF-β was increased while that for IFN-γ was decreased in the mesenteric lymph nodes of piglets treated with L. reuteri every 4^th day. In conclusion, early intervention with L. reuteri increases the presence of beneficial bacteria and decreases the presence of undesirable microbes in the lower gastrointestinal tract. The changes appear to be mediated by altering the intestinal pH through lactic acid production resulting in favorable bacterial species colonization. A prolonged duration of treatment (i.e. every 4^th day) would appear to be superior to treatment only during the first 4 days.

Analysis of the bacterial community in chronic obstructive pulmonary disease sputum samples by denaturing gradient gel electrophoresis and real-time PCR

Background

The Global Initiative defines COPD for chronic obstructive lung disease as an entirely preventable and treatable disease characterized by sputum production, bacterial colonisation, neutrophilic bronchial airway inflammation and poor health status. The World Health Organization (WHO) estimates that COPD will become the fourth-most common cause of death worldwide, just behind ischemic heart disease, cerebrovascular disease and HIV/AIDS, by 2030. The aim of this study was to determine the main structure feature of sputum potentially pathogenic microorganisms in subjects with COPD during the clinical stable state.

Methods

We employed a molecular genetics-based investigation of the bacteria community, including DNA isolation, PCR amplification and DGGE profiling. PCR-denaturing gradient gel electrophoresis (DGGE) with universal primers targeting the V3 region of the 16S rRNA gene was employed to characterize the overall COPD patient sputum microbiota composition, and some excised gel bands were cloned for sequencing. Real-time PCR was further utilized to quantitatively analyze the subpopulation of microbiota using group-specific primers targeting Streptococcus pneumoniae, Klebsiella pneumoniae, Pseudomonas aeruginosa.

Results

The DGGE profiles of two groups displayed significant differences between COPD and healthy groups (P < 0.05). Real-time PCR revealed significant increases of Streptococcus pneumoniae, Klebsiella pneumoniae and Pseudomonas aeruginosa (P < 0.05) in the COPD group compared with the healthy group.

Conclusion

This study revealed strong relationship between alterations of sputum microbiota and COPD. By determining the content of several types of bacteria, we can provide evidence to aid in the diagnosis and treatment of COPD.

The influence of whole grain products and red meat on intestinal microbiota composition in normal weight adults: a randomized crossover intervention trial

Intestinal microbiota is related to obesity and serum lipid levels, both risk factors for chronic diseases constituting a challenge for public health. We investigated how a diet rich in whole grain (WG) products and red meat (RM) influences microbiota. During a 10-week crossover intervention study, 20 healthy adults consumed two isocaloric diets, one rich in WG products and one high in RM. Repeatedly data on microbiota were assessed by 16S rRNA based denaturing gradient gel electrophoresis (DGGE). A blood sample and anthropometric data were collected. Mixed models and logistic regression were used to investigate effects. Microbiota showed interindividual variability. However, dietary interventions modified microbiota appearance: 8 bands changed in at least 4 participants during the interventions. One of the bands appearing after WG and one increasing after RM remained significant in regression models and were identified as Collinsella aerofaciens and Clostridium sp. The WG intervention lowered obesity parameters, while the RM diet increased serum levels of uric acid and creatinine. The study showed that diet is a component of major relevance regarding its influence on intestinal microbiota and that WG has an important role for health. The results could guide investigations of diet and microbiota in observational prospective cohort studies. Trial registration: ClinicalTrials.gov NCT01449383.

Performance and microbial response during the fast reactivation of Anammox system by hydrodynamic stress control

Anaerobic ammonium oxidation (Anammox) has become a promising method for biological nitrogen removal. However, this biotechnology application is always limited due to the low growth rate and biomass yield of Anammox bacteria. This study investigated the process of fast reactivation of an Anammox consortium idled for 2 years via hydrodynamic stress control. The results showed that the Anammox system was efficiently and quickly reactivated by shortening of the hydraulic retention time (HRT) of the reactor from 12 to 6 hr within 68 days of operation. Moreover, at a 4-hr HRT with an influent total nitrogen loading rate of 1.2kg N/(m(3)·day), the reactor maintained high biological performance with an ammonium removal loading rate of 0.52kg N/(m(3)·day) and a nitrite removal rate of 0.59kg N/(m(3)·day). In the reactivated Anammox reaction, the stoichiometric coefficients of NH4(+)-N to NO2(-)-N and NH4(+)-N to NO3(-)-N were 1:1.04±0.08 and 1:0.31±0.03, respectively. The specific Anammox activity and hydrazine oxidoreductase activity, both of which represent the degree of Anammox bacteria present, increased as the hydrodynamic stress increased and were maximally (125.38±3.01mg N/(g VSS·day) and 339.42±6.83μmol/(min·g VSS), respectively) at 4-hr HRT. Microbial response analysis showed that the dominant microbial community was obviously shifted and the dominance of Anammox bacteria was enhanced during the hydrodynamic selection.

The ecological roles of Bacillus thuringiensis within phyllosphere environments

Bacillus thuringiensis (Bt) is one of the most used bio-control agents to control plant insects, but little is known about its effect on the microbial population and communities on plant leaves. With the culture dependent method, it has been observed that the dynamics of Bt within the phyllosphere varied dependent on both the doses of Bt sprayed on the leaves and the plant species, however, Bt's population size kept stable at about 1000 cfu g(-1) after 15 d since inoculation. By comparing the bacterial abundances and community structures within the phyllosphere of three plant species, we confirmed that Bt at the doses of 1.5×10(7) and 1.5×10(9) cfu mL(-1) respectively did not significantly influence the natural bacterial population size on the leaf surfaces based on culture dependent assay. However, based on culture independent denaturing gradient gel electrophoresis (DGGE), Shannon-Wiener index (H') and Unweighted Pair Group Method with Arithmetic Mean (UPGMA) analysis, Bt has a significant influence on the bacterial communities within the phyllosphere of amaranth and cotton, but not rice. These results indicate that Bt exhibits different behaviors and ecological roles on the microbial diversity within the phyllosphere, and its environmental safety has to be concerned and evaluated in the future.